---
title: "June, 2018"
date: 2018-06-04T19:49:54-07:00
author: "Alan Orth"
tags: ["Notes"]
---

## 2018-06-04

- Test the [DSpace 5.8 module upgrades from Atmire](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560) ([#378](https://github.com/ilri/DSpace/pull/378))
  - There seems to be a problem with the CUA and L&R versions in `pom.xml` because they are using SNAPSHOT and it doesn't build
- I added the new CCAFS Phase II Project Tag `PII-FP1_PACCA2` and merged it into the `5_x-prod` branch ([#379](https://github.com/ilri/DSpace/pull/379))
- I proofed and tested the ILRI author corrections that Peter sent back to me this week:

```
$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
```

- I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in [March, 2018]({{< relref "2018-03.md" >}})
- Time to index ~70,000 items on CGSpace:

```
$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b                                  

real    74m42.646s
user    8m5.056s
sys     2m7.289s
```

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## 2018-06-06

- It turns out that I needed to add a server block for `atmire.com-snapshots` to my Maven settings, so now the Atmire code builds
- Now Maven and Ant run properly, but I'm getting SQL migration errors in `dspace.log` after starting Tomcat
- I've updated my ticket on Atmire's bug tracker: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560

## 2018-06-07

- Proofing 200 IITA records on DSpace Test for Sisay: [IITA_Junel_06 (10568/95391)](https://dspacetest.cgiar.org/handle/10568/95391)
  - Mispelled authorship type: CGAIR single center should be: CGIAR single centre
  - I see some encoding errors in author affiliations, for example:
    - Universidade de SÆo Paulo
    - Institut National des Recherches Agricoles du B nin
    - Centre de Coop ration Internationale en Recherche Agronomique pour le D veloppement
    - Institut des Recherches Agricoles du B nin
    - Institut des Savannes, C te d' Ivoire
    - Institut f r Pflanzenpathologie und Pflanzenschutz der Universit t, Germany
    - Projet de Gestion des Ressources Naturelles, B nin
    - Universit t Hannover
    - Universit F lix Houphouet-Boigny
- I uploaded fixes for all those now, but I will continue with the rest of the data later
- Regarding the SQL migration errors, Atmire told me I need to run some migrations manually in PostgreSQL:

```
delete from schema_version where version = '5.6.2015.12.03.2';
update schema_version set version = '5.6.2015.12.03.2' where version = '5.5.2015.12.03.2';
update schema_version set version = '5.8.2015.12.03.3' where version = '5.5.2015.12.03.3';
```

- And then I need to ignore the ignored ones:

```
$ ~/dspace/bin/dspace database migrate ignored
```

- Now DSpace starts up properly!
- Gabriela from CIP got back to me about the author names we were correcting on CGSpace
- I did a quick sanity check on them and then did a test import with my [`fix-metadata-value.py`](https://gist.github.com/alanorth/df92cbfb54d762ba21b28f7cd83b6897) script:

```
$ ./fix-metadata-values.py -i /tmp/2018-06-08-CIP-Authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3
```

- I will apply them on CGSpace tomorrow I think...

## 2018-06-09

- It's pretty annoying, but the JVM monitoring for Munin was never set up when I migrated DSpace Test to its new server a few months ago
- I ran the tomcat and munin-node tags in Ansible again and now the stuff is all wired up and recording stats properly
- I applied the CIP author corrections on CGSpace and DSpace Test and re-ran the Discovery indexing